Package index • bmfaToolkits

All functions

available_backends(): Check which backends are installed and usable
backend_script_dir(): Get the installed directory for a script-based backend
bifa_extdata: Example data shipped in extdata
fit_blast(): Fit BLAST (script backend)
fit_bmsfa(): Fit BMSFA via MSFA::sp_msfa
fit_bmsfa_2step(): Fit BMSFA all-at-once If post_fit0 is NULL, fit an initial BMSFA with given k and j_s, then automatically select the number of factors and refit. Otherwise, use the post_fit0 then select the number of factors and refit.
fit_cavi(): Fit VI-MSFA CAVI (variational MSFA)
fit_cavi_2step(): Fit CAVI with automatic factor selection (2-step)
fit_ind_fa(): Fit independent factor analysis (Ind FA) via MSFA::sp_fa (per study)
fit_ind_fa_2step(): Fit Ind FA all at once If post_fit0 is NULL, fit an initial IndFA with given j_s, then automatically select the number of factors and refit.
fit_integrative_fa(): Fit an integrative factor model with a chosen method within a general interface
fit_momss(): Fit MOM-SS (MOM-SS / BFR.BE backend)
fit_pfa(): Fit PFA (Perturbed Factor Analysis; script backend)
fit_stack_fa(): Fit stacked factor analysis (Stack FA) via MSFA::sp_fa
fit_stack_fa_2step(): Fit Stack FA all-at-once If post_fit0 is NULL, fit an initial StackFA with given k, then automatically select the number of factors and refit.
fit_sufa(): Fit SUFA
fit_tetris(): Fit Tetris (single run)
fit_tetris_2step(): Run the full Tetris pipeline: initial fit -> choose T -> fixed refit
install_backend(): Install optional backends used in the tutorial
load_backend(): Load a bundled script backend into a private environment
load_curated_ovarian(): Load curated ovarian data (Bioconductor)
load_simulated_nutrition_data(): Load the simulated nutrition dataset from this package
load_toy(): Load the toy example object
load_toy_data(): Load the toy dataset from this package
plot_single_loadings(): Plot a loading matrix as a heatmap
postprocess_bmsfa(): Post-process BMSFA output
postprocess_ind_fa(): Post-process Ind FA output (nutrition tutorial)
postprocess_integrative_fa(): Post-process an integrative factor model fit
postprocess_momss(): Post-process MOM-SS output
postprocess_pfa(): Post-process PFA output (nutrition tutorial)
postprocess_stack_fa(): Post-process Stack FA output (nutrition tutorial)
postprocess_sufa(): Post-process SUFA output
postprocess_tetris(): Post-process Tetris output
post_BLAST() postprocess_blast(): Post-process BLAST output into a standard format
post_CAVI() postprocess_cavi(): Post-process CAVI output into a standard format
refit_cavi(): Refit CAVI after selecting the number of factors
select_js_bmsfa(): Select J_s for BMSFA from study-specific covariances
select_js_cavi(): Select J_s for CAVI from study-specific covariances
select_js_ind_fa(): Select J_s for Ind FA (per-study) using eigen proportion rule
select_k_bmsfa(): Select K for BMSFA from common covariance
select_k_cavi(): Select K for CAVI from the common covariance
select_k_from_sigma(): Select number of factors via eigenvalue proportion rule
select_k_pfa(): Select K for PFA via nontrivial-column rule
select_k_stack_fa(): Select K for Stack FA using eigen proportion rule
select_T_tetris(): Select big_T (A matrix) for Tetris